Metaxas has received some criticism, not just from those who disagree with him about whether or not God exists, but also from some who are Christian theists yet think using science in this way is a misguided approach (see this piece by philosopher Francis Beckwith).
Without getting into the details of either the argument itself, or the arguments about the argument, I was reminded of the following advice from C.S. Lewis:
"If you know any science it is very desirable that you should keep it up. We have to answer the current scientific attitude towards Christianity, not the attitude which scientists adopted one hundred years ago. Science is in continual change and we must try to keep abreast of it. For the same reason, we must be very cautious of snatching at any scientific theory which, for the moment, seems to be in our favour. We may mention such things; but we must mention them lightly and without claiming that they are more than 'interesting'. Sentences beginning 'Science has now proved' should be avoided. If we try to base our apologetic on some recent development in science, we shall usually find that just as we have put the finishing touches to our argument science has changed its mind and quietly withdrawn the theory we have been using as our foundation stone" (God in the Dock, p. 92).I don't mean to suggest the above as either a criticism or defense of the article by Metaxas. But I don't see that he has claimed "Science has now proved God," but rather that it points to God. And there is a distinction between employing arguments that employ contemporary science as part of a cumulative case for God's existence, and using a particular scientific theory "as our foundation stone". Beckwith is right that philosophy is where we should begin when doing natural theology. But I think there is nothing wrong with pointing out that some findings of contemporary science point towards the truth of theism, rather than atheism.
When making cumulative case arguments for theism, over the years (and the generations) we'll be adding new stones and removing others, whether these stones are philosophical, empirical, or personal. The empirical data and their interpretation have a place, as Metaxas argues, but such stones should not be used as our foundation stone, as Lewis points out. For me, the foundation is philosophical, theological, and personal, in a particular sense of each of these terms.